comparison lib.r @ 25:1de8423cd6a9 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:20:42 -0400
parents 5c62dfdb64f4
children 14b1c52fae62
comparison
equal deleted inserted replaced
24:9a0ca3f3a847 25:1de8423cd6a9
331 exists <- file.exists(files_abs) 331 exists <- file.exists(files_abs)
332 files[exists] <- files_abs[exists] 332 files[exists] <- files_abs[exists]
333 files[exists] <- sub("//","/",files[exists]) 333 files[exists] <- sub("//","/",files[exists])
334 334
335 # WHAT IS ON THE FILESYSTEM 335 # WHAT IS ON THE FILESYSTEM
336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) 336 filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] 337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
338 338
339 # COMPARISON 339 # COMPARISON
340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { 340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) 341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())